MmuINT0078197 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152435342-152440323:-
Coord C1 exon
chr1:152440086-152440323
Coord A exon
chr1:152435405-152440085
Coord C2 exon
chr1:152435342-152435404
Length
4681 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
TGCTTTTCTCTCTTTGGTAGGAG
3' ss Score
8.28
Exon sequences
Seq C1 exon
GATTACACAGAGGACTACATTCAAACAGGACCCGGTCAGCTCTATGCCTACTCAACTCGTCTGTTCACCATCGATGGCATCAGTATCCCCTATACGTGGAACCACACCATTTTCTATGATCAGGCCTGGGGGAAAATGCCTTTCTTAGTAGAGACACTTCATGCATCTTCCATAGAGTCTGACTACAACCAACTAGAAGAGACACTGGGTTTTAAAATCCATGCTTCAATTTCCAAAG
Seq A exon
GTAACATTGTTAAGGGAACCTCCAAAGATCTGTGCTGCCGTCTTATTTTTTTTTAGAAAGATAAAGATAGGTGCCTTGAAGCCATTCAAATTAGGAATATGAAGGGCCAGGTCTAACATGCTGGAGTTGGGTTTTTTGTCTGTGCTACATTCTGTTTTTGTTGTAGGAAGGCCCTTGTAAAGCTCACTCAGTTGCATTTGGTTGACTAAGATGCCTCTCCAGGCAACCTAGGCAACCAGACAAAGTCCTAACCCAGATTCTTGGACAGGACTAAATGTTATCCACCTGAAGGGTTTTTCTTTAGGTAATACAGTCCATTTTTAAATACTGTCTTAATTGATGAATTTTCAAAATTCAAAATTACTGATGTAAAGTACACCCCAGCTTAAACTAATCAGAAATTTCTAGATTTTTCAAGGCAGCTTCCTTTAAGTGCTTTATTCTCTGTATTGAATATATTGATGTTGTCTTTTGGGAAGGCCCAACATGTATGTGTCAAGCAGAGCTATAACACTGAGGAAATGGGGAAACAAAAGAATTCACATTAATACACCTTAGAACACTTAGAACTTAGTAATGTGGCCATAATGTTTATCATCCCAACCAAGACTCCTGTGAGAAAAAGAGTCAGTATTGCAATGAAATTTTTTCTGGAAAAATTAGAACATCTAGTCGCCCTGGGTAAAGGTGGCTATCAGGCACTGTGGAGCAATAGTTATTATACTATTACTCCTCATCCATGGAAATCATCATCTAAGACATGGCTTCTGAACTGTTCTCTGTTGTCTGGTAGTCCTACATCTCCATCAAGGCAGTGCCCCGTGATGTGCGCTTGCTTGAAGTGTCTGGTCCCCAGATTTCCTTCTCCATCTTCAAAACCACCTTCAAAACCACTGCTGCCGTCAGTTCCATATTCTGTGGACTTTGGGAGTTGTTTTGTTTTGTTTTGTTTACTTCTGTTTTGTTTTGGTTTGGTTTGGTTTTTTTGGTAACTCAATTGTGTAGTTCTCTTTTTATAAAAAGAACTCTTTTTACCCAGGTAGAGTGTTGACTGTGTTCTAAGCTCAGCGCTTCTCCACGGCATGATGGTAGTAGCCGACTACAAACACGGCCCCTTCCATGCCCTCTTCACTCAGCAGTCCACACAATGTGTACACAACTTCCCTCAGTTGTTACTTTGTAGCGCCACTACTCAGACCTGTTGGTTGCAAAGCTCGTGATCACAAGCTTCGTAGAGCAGTAAATGCTGGTGCAGCGTCAAAAGGTTGGACATGCTTGACGAACTGAAATGATTGCTGAGATGGGCATGTATGTGTACTTCTACATGTTAGGCTTGTTAGCATGTAACACGTTAAATGCTAAGCTTAAAGCCAACTGGACATCTTTGCACCATCTCTGAGACTGTGGCTGAACAGTCTGCGTCCCAGAATATAAGTAAACACAGTTCAATTGTGTTGCAGTCCTTGGGGGTATGTGTCTCTGATATGGGAGTTACATTTGAAAGATGTGCCTGCAGTTTCTCAGTAACCACCAGGGGGCAAACTTGCATTCTGGGTCACTCAACACATTTTCAATGCTCAAAATCCATCCTAACTAAATCACAGAAACAACCCAACAGGACTATTTTTAGAGATTTCACCTAGTGTTCTTTATAATAGAAAAATAGTAAATGAATATCTCAGAAACTTGAAATAAATAAATGAAATAGGAAATTGTGACGTGTTTAATAATCTCATAATAATAATCTAATAATAAGAGTCATTGAAATGAGTTTCAAGAAATAGTTGATTCATATTTTTTTAGGAACAGTTGTGGGGTGCCTGTCATGTAGCAGGCCCCACTGCAAGCTTACTCACAGGATAAGGAGCACACTTATGTTATAATAGTGACTGAGAGGCAGTGTGCGCACGCACACACAGCTTGCATTTCTGATTGTATGGAAATATTCCCATGATTAAAAACAAATAATTTGTCTTTTCCTTGACAATTATTATATCGGATGAAAGCATCTCCATTGCGTGTGTGTGTGTGTGTGTGTGTGCGTGCATGCGCACGTGTGTGCATGCATGCATACACACACTTGTGCACACATGAATGCCACAGCAGTTATGCAGTGGTCAGAGGACACTTGCAGACATCAGTTCCTTCTTCCCCTCGGTATCAAACTCAGGACTTAAATGTTGGCAGAGAGCACCTTGCCGTATTTTCTGTACAAAAATCTACATCTTAAATAAGTTCTCTAAATGATTTTTTTTATTCAAAAAGCTTGGTAATTACTAGTCAATAATTTCATACTTACCATTTTAAGTATAGATTAATTAAAATGGCAAGAAAAAAAAGTCCATGTTTCGAGAAACTGAAACAGTTTGTTCCTACTGATAAAGTTATAGGGAAATTTACTTCAGACTTTCAAATTTTCTACTATTACATTATTATAATCACAAACAAATATTTTTGTATTTTCTCCTATCTTCATCTCCTGATGAAATTCACAGCTATAGTTCAAAATAATCTACTTGTACTGTAAGATAAAGAATGAGTGGCAGATGAGACGGCCCAGGGGGCAATGGTACTTGCCACCAAGCCTGATGACCTAAATGTGGGAAAGGAGATCCACCAAGCTGTTCTCTGATCTTCATGTGAGCACTGTGGCACACAGGCACCCACAACACAGATGTACACGCAAATAAAAAAAAATCAATAAAAATGGAGCTAGAGAGACATCTGAGTGGAGCCTTTTCTATACAAGCATAAAGACTTGAGTTTGGATCTTCAGAACCCAGTTAAAACGCTATGCACTGAGGCACATGTCTGTATCCCTGCCAGAGAAGCTATAACAGGATCCTGGAGGCTCCGAGCCAACTAATGTAGTAAAAATGGCAAGCTTTTGGTTCAGTAAGAGAGAGAGAAATACCTTAGCTCAAGAATGAATGAATAAATGAACAAACAAACAAACAAATAAGGTAGCTAGCTGAGGTTGACGGAAAACATCATAGCATCAACATCTATATTCCATACACTCAAGCACAGACAAGTGTACCCACACACATGTGTGTGCAAACACATATATCCACCACACATACACATGAAAAGAAAGGAATAAATAAGTGAAAATAATTCATAATGCAATATTGTGTTTTAATGTGAGAATTTTTGAAAAAAGAAAACTAAGACCATTCCTAAACTTACCTGTAAAATCCTACTTTCTCAGTGGATGGGTAACTTAAGAAATCCTTTGTTACATTCTCAATAAAATGAAGAATAATAAGATATAAATTCATGATAGTTATATTCCTAAAAAAATAGGTTTCATATTTAAATCCCATGAAAATGTTTGCTACGTGGTACATACATTCAACGCTTTTATAATCGCGGCCTCCTTTGTACATTAAAATCTTTCAGAAGAAAGAACAAAAGGTCAGGTCTTTCCTACACATCTCAGAATTGTTGAAATCTGTCTCCAGGCCTTCCCCCATTCACTGGGCTTTTCTTTTAAAAATTTTTTTCTACTAGGAATTCCCTGTGATCGCCTGGGTTGACCTCAAACAGACTGCCGTGCTTCCTCACCCTCTCGGGAGCTGGCATTGCAGGCGTGAGCCACCACACTGAGCTCCATGCTCTGAGCTATAATAGTCCTCCTTACGTGGTGGCATACAAGAAATCTCCTCCCGCAAAATCCCCCAAAGGGTAGCTAATGAAAATATCTTTCCTGACTAAATCCAAAAAATGCAAAGCTCCTATATGATAATTAATCTTCTCTCTATGACACGATTTTTTGCAAGTTTATTCCCACCATGGTACCATACACACATACTGGTTAAGTTTAAAGATCATAGGAATGTATGAATAACTGAACATAAGTTGTGACAATCAATTCAGCAGGTGAAAGTCAACGAGGCTTTCCCCTTAAGCCTGACCATGGTAGCTTTTGCTCTTAAGCACTTTATAAGATGTTACTCTCAGACTCTTCATCTGAAAACTAGGTATCATGACAGCAGTAAAGATGTCCTGTGGATTAAATGAAATGAAGCAGATGGTGACCTTCACATACTACATGCCAAGGATGCTTTTGCCCCGCCCACCTTATTCCCACTCCTTTCCCGATGACTGGGATGCTATTGGGAAAGAGTTAAATTTGCTCTAGCTCAGCTTGCCTGCCACCCTTGGTTCAATTGCTCAGAACAGTAAGACAGTCACATGTAGAATTTTGGCTAAGATTCTCAACATCACAAATGGAGAAGACCGAGAAATAAATGGGGACTTCTAGCTCAAATGTTGATTTTCCACTGTAGCAACTTCAGTTGCTTGCACACAACATCCTTCGTCCTTCAATGAAAATCTACCAGTGGTTGGAACAACGGAATGCACCTGTAGCTGTGCCCAACGCATAGTTTATCTTGGGTTCTCTTTAGCTATTACAGAGTGGCTTATTTTGTTTTCTTTTTATTGCTGTATATAACTTAAACAGAAACTGTTTCCAGTGTCAGCTTGCCAACAATATCTGGACTAGTTCATTTACCTCTTGGTTGAAGAAACATGAAGTTCTCCTTTCTTTTCTGTTTCTAATACTGTATTTTTCATTGTTCCTTCTTTGATGCATCTTCCCAGAGAAGGCCATACTAGAATGAAAAGTGCCAGTCTTCTAACGAGTCAGTTAATTGTGCTTTTCTCTCTTTGGTAG
Seq C2 exon
GAGATCGCAGTAACCAGTGCCCCTCTGGGTTCATTTTAGACTCGGTTGGACCCTTTTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:97
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF074747=G2F=PD(26.1=61.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: